cellprofiler-library-nightly 5.0.0.dev643__tar.gz → 5.0.0.dev644__tar.gz

{cellprofiler_library_nightly-5.0.0.dev643/cellprofiler_library_nightly.egg-info → cellprofiler_library_nightly-5.0.0.dev644}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev643
+Version: 5.0.0.dev644
 Summary: cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
 Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
 Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>

{cellprofiler_library_nightly-5.0.0.dev643 → cellprofiler_library_nightly-5.0.0.dev644}/cellprofiler_library/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev643'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev643')
+__version__ = version = '5.0.0.dev644'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev644')
 
-__commit_id__ = commit_id = 'g229e6671e'
+__commit_id__ = commit_id = 'g02a8b5144'

{cellprofiler_library_nightly-5.0.0.dev643 → cellprofiler_library_nightly-5.0.0.dev644}/cellprofiler_library/functions/measurement.py

@@ -1692,6 +1692,33 @@ def measure_quartile_intensity(indices:NDArray[numpy.int_], areas: NDArray[numpy
     dest_no_upper = limg[order[qindex[qmask_no_upper]]]
     return qmask, _dest, qmask_no_upper, dest_no_upper
 
+def measure_mad_intensity(
+        limg: NDArray[Pixel],
+        llabels: NDArray[ObjectLabel],
+        lindexes: NDArray[numpy.int_],
+        median_intensity: NDArray[numpy.float_],
+        ) -> NDArray[numpy.float64]:
+    """Compute the median absolute deviation (MAD) of intensity per object.
+
+    MAD is defined as median(|x_i - median(x)|). Unlike the quartile measurements,
+    this is computed as a true per-object median of the absolute deviations rather
+    than via interpolated quartile indexing, which would otherwise interpolate
+    across value boundaries for odd-sized objects and yield an incorrect result.
+
+    Args:
+        limg: 1D array of object pixel intensities
+        llabels: 1D array of object labels, aligned with ``limg``
+        lindexes: object label indices to compute over
+        median_intensity: per-object median intensity, indexed by label - 1
+
+    Returns:
+        Array of MAD values, one per entry in ``lindexes``.
+    """
+    madimg = numpy.abs(limg - median_intensity[llabels - 1])
+    return centrosome.cpmorphology.fixup_scipy_ndimage_result(
+        scipy.ndimage.median(madimg, llabels, lindexes)
+    )
+
 ###############################################################################
 # MeasureObjectOverlap
 ###############################################################################

{cellprofiler_library_nightly-5.0.0.dev643 → cellprofiler_library_nightly-5.0.0.dev644}/cellprofiler_library/modules/_measureobjectintensity.py

@@ -7,7 +7,7 @@ from pydantic import Field, validate_call, ConfigDict, BaseModel
 from cellprofiler_core.utilities.core.object import crop_labels_and_image
 from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask, ObjectLabelSet, Pixel, ObjectLabel
 from cellprofiler_library.measurement_model import LibraryMeasurements
-from cellprofiler_library.functions.measurement import measure_object_area_occupied, measure_integrated_intensity, measure_mean_intensity, measure_std_intensity, measure_min_intensity, measure_max_intensity, measure_max_position, measure_center_of_mass_binary, measure_center_of_mass_intensity, measure_mass_displacement, measure_quartile_intensity
+from cellprofiler_library.functions.measurement import measure_object_area_occupied, measure_integrated_intensity, measure_mean_intensity, measure_std_intensity, measure_min_intensity, measure_max_intensity, measure_max_position, measure_center_of_mass_binary, measure_center_of_mass_intensity, measure_mass_displacement, measure_quartile_intensity, measure_mad_intensity
 from cellprofiler_library.opts.measureobjectintensity import TemplateMeasurementFormat, IntensityFeature
 
 
@@ -216,15 +216,14 @@ def measure_object_intensity(
                 dest[lindexes[qmask_no_upper] - 1] = _dest_no_upper
 
             #
-            # Once again, for the MAD
+            # The MAD = median(|x_i - median(x)|). Compute it as a true
+            # per-object median of the absolute deviations. Reusing the
+            # quartile machinery here would interpolate across value
+            # boundaries for odd-sized objects and give a wrong result.
             #
-            fraction = 1.0/ image_dimensions
-            madimg = numpy.abs(limg - median_intensity[llabels - 1])
-            order = numpy.lexsort((madimg, llabels))
-
-            qmask, _mad_intensity, qmask_no_upper, _mad_intensity_no_upper = measure_quartile_intensity(indices, areas, fraction, madimg, order)
-            mad_intensity[lindexes[qmask] - 1] = _mad_intensity
-            mad_intensity[lindexes[qmask_no_upper] - 1] = _mad_intensity_no_upper
+            mad_intensity[lindexes - 1] = measure_mad_intensity(
+                limg, llabels, lindexes, median_intensity
+            )
 
         emask = masked_outlines > 0
         eimg = img[emask]

{cellprofiler_library_nightly-5.0.0.dev643 → cellprofiler_library_nightly-5.0.0.dev644/cellprofiler_library_nightly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev643
+Version: 5.0.0.dev644
 Summary: cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
 Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
 Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>